source: issm/trunk-jpl/src/m/classes/model.m@ 21808

Last change on this file since 21808 was 21808, checked in by schlegel, 8 years ago

Add capability for regional output definitions
File size: 66.3 KB
RevLine 
[8926]1%MODEL class definition
2%
3% Usage:
4% md = model(varargin)
5
6classdef model
[13692]7 properties (SetAccess=public) %Model fields
8 % {{{
9 %Careful here: no other class should be used as default value this is a bug of matlab
10 mesh = 0;
11 mask = 0;
[9778]12
[13692]13 geometry = 0;
14 constants = 0;
[19527]15 smb = 0;
[13692]16 basalforcings = 0;
17 materials = 0;
[16160]18 damage = 0;
[13692]19 friction = 0;
20 flowequation = 0;
21 timestepping = 0;
22 initialization = 0;
23 rifts = 0;
[19984]24 slr = 0;
[9778]25
[13692]26 debug = 0;
27 verbose = 0;
28 settings = 0;
[14621]29 toolkits = 0;
[13692]30 cluster = 0;
[9778]31
[13692]32 balancethickness = 0;
[17757]33 stressbalance = 0;
[13692]34 groundingline = 0;
35 hydrology = 0;
[17757]36 masstransport = 0;
[13692]37 thermal = 0;
38 steadystate = 0;
39 transient = 0;
[20460]40 levelset = 0;
[18757]41 calving = 0;
[21584]42 gia = 0;
[21260]43 esa = 0;
[9778]44
[13692]45 autodiff = 0;
46 inversion = 0;
47 qmu = 0;
[21674]48 amr = 0;
[8926]49
[13692]50 results = 0;
[16388]51 outputdefinition = 0;
[13692]52 radaroverlay = 0;
53 miscellaneous = 0;
54 private = 0;
[9778]55
[13692]56 %}}}
57 end
58 methods (Static)
59 function md = loadobj(md) % {{{
60 % This function is directly called by matlab when a model object is
61 % loaded. If the input is a struct it is an old version of model and
62 % old fields must be recovered (make sure they are in the deprecated
63 % model properties)
[8926]64
[13692]65 if verLessThan('matlab','7.9'),
66 disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
67 disp(' if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');
[8952]68
[13692]69 % This is a Matlab bug: all the fields of md have their default value
70 % Example of error message:
71 % Warning: Error loading an object of class 'model':
72 % Undefined function or method 'exist' for input arguments of type 'cell'
73 %
74 % This has been fixed in MATLAB 7.9 (R2009b) and later versions
75 end
[8952]76
[13692]77 if isstruct(md)
78 disp('Recovering model object from a previous version');
79 md = structtomodel(model,md);
80 end
[13239]81
[13692]82 %2012 August 4th
83 if isa(md.materials,'materials'),
84 disp('Recovering old materials');
85 if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
[13718]86 md.materials=matice(md.materials);
87 else
[13692]88 md.materials=matdamageice(md.materials);
89 end
90 end
[14559]91 %2013 April 12
[15771]92 if numel(md.stressbalance.loadingforce==1)
93 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14559]94 end
[14618]95 %2013 April 17
96 if isa(md.hydrology,'hydrology'),
97 disp('Recovering old hydrology class');
98 md.hydrology=hydrologyshreve(md.materials);
99 end
[16356]100 %2013 October 9
101 if ~isa(md.damage,'damage'),
102 md.damage=damage();
103 md.damage.D=zeros(md.mesh.numberofvertices,1);
104 md.damage.spcdamage=NaN*ones(md.mesh.numberofvertices,1);
105 end
[16822]106 %2013 November 18
107 if ~isa(md.outputdefinition,'outputdefinition'),
108 md.outputdefinition=outputdefinition();
109 end
[17558]110 %2014 March 26th
111 if isa(md.mesh,'mesh'),
[17566]112 disp('Recovering old mesh class');
113 if isprop(md.mesh,'dimension'),
114 if md.mesh.dimension==2,
115 md.mesh=mesh2d(md.mesh);
116 else
117 md.mesh=mesh3dprisms(md.mesh);
118 end
[17558]119 else
[17566]120 md.mesh=mesh2dvertical(md.mesh);
[17558]121 end
122 end
[18775]123 %2014 November 12
[21702]124 if isa(md.calving,'double'); md.calving=calving(); end
[20059]125 %2016 February 3
[21702]126 if isa(md.slr,'double'); md.slr=slr(); end
[21260]127 %2016 October 11
[21702]128 if isa(md.esa,'double'); md.esa=esa(); end
[21545]129 %2017 February 10th
130 if md.settings.solver_residue_threshold==0,
131 md.settings.solver_residue_threshold = 1e-6;
132 end
[21667]133 %2017 April 10th
[21702]134 if isa(md.gia,'gia'), md.gia=giaivins(); end
135 %2017 May 4th
136 if isa(md.amr,'double'); md.amr=amr(); end
[20460]137
[13692]138 end% }}}
139 end
140 methods
141 function md = model(varargin) % {{{
[8926]142
[13692]143 switch nargin
144 case 0
145 md=setdefaultparameters(md);
[18492]146 case 1
[19087]147 error('model constructor not supported yet');
[18503]148
[13692]149 otherwise
150 error('model constructor error message: 0 of 1 argument only in input.');
151 end
152 end
153 %}}}
154 function md = checkmessage(md,string) % {{{
155 if(nargout~=1) error('wrong usage, model must be an output'); end
156 disp(['model not consistent: ' string]);
157 md.private.isconsistent=false;
158 end
159 %}}}
160 function md = collapse(md)% {{{
161 %COLLAPSE - collapses a 3d mesh into a 2d mesh
162 %
163 % This routine collapses a 3d model into a 2d model
164 % and collapses all the fileds of the 3d model by
165 % taking their depth-averaged values
166 %
167 % Usage:
168 % md=collapse(md)
169 %
170 % See also: EXTRUDE, MODELEXTRACT
[13005]171
[13692]172 %Check that the model is really a 3d model
[17687]173 if ~strcmp(md.mesh.elementtype(),'Penta'),
[13692]174 error('collapse error message: only 3d mesh can be collapsed')
175 end
[13005]176
[17724]177 %Start with changing all the fields from the 3d mesh
[13005]178
[18775]179 %dealing with the friciton law
[13692]180 %drag is limited to nodes that are on the bedrock.
[18775]181 if isa(md.friction,'friction'),
182 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
183 md.friction.p=project2d(md,md.friction.p,1);
184 md.friction.q=project2d(md,md.friction.q,1);
185 elseif isa(md.friction,'frictionhydro'),
186 md.friction.q=project2d(md,md.friction.q,1);
187 md.friction.C=project2d(md,md.friction.C,1);
188 md.friction.As=project2d(md,md.friction.As,1);
[18798]189 md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
[18775]190 elseif isa(md.friction,'frictionwaterlayer'),
191 md.friction.coefficient=project2d(md,md.friction.coefficient,1);
192 md.friction.p=project2d(md,md.friction.p,1);
193 md.friction.q=project2d(md,md.friction.q,1);
194 md.friction.water_layer=project2d(md,md.friction.water_layer,1);
195 elseif isa(md.friction,'frictionweertman'),
196 md.friction.C=project2d(md,md.friction.C,1);
197 md.friction.m=project2d(md,md.friction.m,1);
[19720]198 elseif isa(md.friction,'frictionweertmantemp'),
199 md.friction.C=project2d(md,md.friction.C,1);
200 md.friction.m=project2d(md,md.friction.m,1);
201 else
202 disp('friction type not supported');
[18775]203 end
[13005]204
[13692]205 %observations
206 if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
207 if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
208 if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
209 if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
210 if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
211 if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
[19527]212 if isa(md.smb,'SMBforcing') & ~isnan(md.smb.mass_balance),
213 md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
214 elseif isa(md.smb,'SMBhenning') & ~isnan(md.smb.smbref),
215 md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
[13692]216 end;
[13005]217
[13692]218 %results
219 if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
220 if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
221 if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
222 if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
[18578]223 if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;
[18506]224 if ~isnan(md.initialization.pressure),md.initialization.pressure=project2d(md,md.initialization.pressure,1);end;
[18578]225 if ~isnan(md.initialization.sediment_head),md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);end;
226 if ~isnan(md.initialization.epl_head),md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);end;
227 if ~isnan(md.initialization.epl_thickness),md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);end;
[21417]228 if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project2d(md,md.initialization.waterfraction,1);end;
229 if ~isnan(md.initialization.watercolumn),md.initialization.watercolumn=project2d(md,md.initialization.watercolumn,1);end;
[21530]230 %giaivins
[21584]231 if ~isnan(md.gia.mantle_viscosity), md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1); end
232 if ~isnan(md.gia.lithosphere_thickness), md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1); end
[15021]233
[13692]234 %elementstype
235 if ~isnan(md.flowequation.element_equation)
236 md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
237 md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
[15564]238 md.flowequation.borderSSA=project2d(md,md.flowequation.borderSSA,1);
239 md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
240 md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
[13692]241 end
[13005]242
[13692]243 %boundary conditions
[15771]244 md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
245 md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
246 md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
247 md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
248 md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
[15767]249 md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
[21544]250 if numel(md.damage.spcdamage)>1, md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers); end
[21417]251 if numel(md.levelset.spclevelset)>1, md.levelset.spclevelset=project2d(md,md.levelset.spclevelset,md.mesh.numberoflayers); end
[13692]252 md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);
[13005]253
[18506]254 % Hydrologydc variables
255 if isa(md.hydrology,'hydrologydc');
256 md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
257 md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
258 md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
259 md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);
260 if(md.hydrology.isefficientlayer==1)
261 md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
[21808]262 end
263 end
[18506]264
[13692]265 %materials
266 md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
267 md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
[16160]268
269 %damage:
[17940]270 if md.damage.isdamage,
271 md.damage.D=DepthAverage(md,md.damage.D);
272 end
[13005]273
[13692]274 %special for thermal modeling:
[18378]275 if ~isnan(md.basalforcings.groundedice_melting_rate),
276 md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1);
277 end
[21417]278 if isprop(md.basalforcings,'floatingice_melting_rate') & ~isnan(md.basalforcings.floatingice_melting_rate),
[18378]279 md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_melting_rate,1);
280 end
[13692]281 md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux
[13005]282
[21417]283 if isprop(md.calving,'coeff') & ~isnan(md.calving.coeff),
284 md.calving.coeff=project2d(md,md.calving.coeff,1);
285 end
286 if isprop(md.calving,'meltingrate') & ~isnan(md.calving.meltingrate),
287 md.calving.meltingrate=project2d(md,md.calving.meltingrate,1);
288 end
289
[13692]290 %update of connectivity matrix
291 md.mesh.average_vertex_connectivity=25;
[13005]292
[13692]293 %Collapse the mesh
294 nodes2d=md.mesh.numberofvertices2d;
295 elements2d=md.mesh.numberofelements2d;
[13005]296
[13692]297 %parameters
298 md.geometry.surface=project2d(md,md.geometry.surface,1);
299 md.geometry.thickness=project2d(md,md.geometry.thickness,1);
[17590]300 md.geometry.base=project2d(md,md.geometry.base,1);
[18480]301 if ~isnan(md.geometry.bed),
302 md.geometry.bed=project2d(md,md.geometry.bed,1);
303 end
[17991]304
[18378]305 if ~isnan(md.mask.groundedice_levelset),
306 md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);
307 end
308 if ~isnan(md.mask.ice_levelset),
309 md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);
310 end
[13005]311
[21808]312 %outputdefinitions
313 for i=1:length(md.outputdefinition.definitions)
314 if isobject(md.outputdefinition.definitions{i})
315 %get subfields
316 solutionsubfields=fields(md.outputdefinition.definitions{i});
317 for j=1:length(solutionsubfields),
318 field=md.outputdefinition.definitions{i}.(solutionsubfields{j});
319 if length(field)==md.mesh.numberofvertices | length(field)==md.mesh.numberofelements,
320 md.outputdefinition.definitions{i}.(solutionsubfields{j})=project2d(md,md.outputdefinition.definitions{i}.(solutionsubfields{j}),1);
321 end
322 end
323 end
324 end
325
[13692]326 %Initialize with the 2d mesh
[17724]327 mesh=mesh2d();
328 mesh.x=md.mesh.x2d;
329 mesh.y=md.mesh.y2d;
330 mesh.numberofvertices=md.mesh.numberofvertices2d;
331 mesh.numberofelements=md.mesh.numberofelements2d;
332 mesh.elements=md.mesh.elements2d;
[21499]333 if numel(md.mesh.lat) ==md.mesh.numberofvertices, mesh.lat=project2d(md,md.mesh.lat,1); end
334 if numel(md.mesh.long)==md.mesh.numberofvertices, mesh.long=project2d(md,md.mesh.long,1); end
335 mesh.epsg=md.mesh.epsg;
[17991]336 if ~isnan(md.mesh.vertexonboundary), mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1); end
337 if ~isnan(md.mesh.elementconnectivity), mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1); end
[17724]338 md.mesh=mesh;
[18738]339 md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
340 md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
[19955]341 md.mesh.segments=contourenvelope(md.mesh);
[13005]342
[13692]343 end % }}}
344 function md2 = extract(md,area) % {{{
345 %extract - extract a model according to an Argus contour or flag list
346 %
347 % This routine extracts a submodel from a bigger model with respect to a given contour
348 % md must be followed by the corresponding exp file or flags list
349 % It can either be a domain file (argus type, .exp extension), or an array of element flags.
350 % If user wants every element outside the domain to be
[15564]351 % extract2d, add '~' to the name of the domain file (ex: '~HO.exp');
[13692]352 % an empty string '' will be considered as an empty domain
353 % a string 'all' will be considered as the entire domain
354 %
355 % Usage:
356 % md2=extract(md,area);
357 %
358 % Examples:
359 % md2=extract(md,'Domain.exp');
360 %
361 % See also: EXTRUDE, COLLAPSE
[13005]362
[13692]363 %copy model
364 md1=md;
[13005]365
[13692]366 %some checks
367 if ((nargin~=2) | (nargout~=1)),
368 help extract
369 error('extract error message: bad usage');
370 end
[13005]371
[13692]372 %get elements that are inside area
373 flag_elem=FlagElements(md1,area);
374 if ~any(flag_elem),
375 error('extracted model is empty');
376 end
[13005]377
[13692]378 %kick out all elements with 3 dirichlets
379 spc_elem=find(~flag_elem);
380 spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
381 flag=ones(md1.mesh.numberofvertices,1);
382 flag(spc_node)=0;
383 pos=find(sum(flag(md1.mesh.elements),2)==0);
384 flag_elem(pos)=0;
[13005]385
[13692]386 %extracted elements and nodes lists
387 pos_elem=find(flag_elem);
388 pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));
[13005]389
[13692]390 %keep track of some fields
391 numberofvertices1=md1.mesh.numberofvertices;
392 numberofelements1=md1.mesh.numberofelements;
393 numberofvertices2=length(pos_node);
394 numberofelements2=length(pos_elem);
395 flag_node=zeros(numberofvertices1,1);
396 flag_node(pos_node)=1;
[13005]397
[13692]398 %Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
399 Pelem=zeros(numberofelements1,1);
400 Pelem(pos_elem)=[1:numberofelements2]';
401 Pnode=zeros(numberofvertices1,1);
402 Pnode(pos_node)=[1:numberofvertices2]';
[13005]403
[13857]404 %renumber the elements (some nodes won't exist anymore)
[13692]405 elements_1=md1.mesh.elements;
406 elements_2=elements_1(pos_elem,:);
407 elements_2(:,1)=Pnode(elements_2(:,1));
408 elements_2(:,2)=Pnode(elements_2(:,2));
409 elements_2(:,3)=Pnode(elements_2(:,3));
[17558]410 if isa(md1.mesh,'mesh3dprisms'),
[13692]411 elements_2(:,4)=Pnode(elements_2(:,4));
412 elements_2(:,5)=Pnode(elements_2(:,5));
413 elements_2(:,6)=Pnode(elements_2(:,6));
414 end
[13005]415
[13857]416 %OK, now create the new model!
[13005]417
[13857]418 %take every field from model
[13692]419 md2=md1;
[13005]420
[13692]421 %automatically modify fields
[13005]422
[13692]423 %loop over model fields
424 model_fields=fields(md1);
425 for i=1:length(model_fields),
426 %get field
427 field=md1.(model_fields{i});
428 fieldsize=size(field);
429 if isobject(field), %recursive call
430 object_fields=fields(md1.(model_fields{i}));
431 for j=1:length(object_fields),
432 %get field
433 field=md1.(model_fields{i}).(object_fields{j});
434 fieldsize=size(field);
435 %size = number of nodes * n
436 if fieldsize(1)==numberofvertices1
437 md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
438 elseif (fieldsize(1)==numberofvertices1+1)
439 md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
[13857]440 %size = number of elements * n
[13692]441 elseif fieldsize(1)==numberofelements1
442 md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
[21428]443 elseif (fieldsize(1)==numberofelements1+1)
444 md2.(model_fields{i}).(object_fields{j})=[field(pos_elem,:); field(end,:)];
[13692]445 end
446 end
447 else
448 %size = number of nodes * n
449 if fieldsize(1)==numberofvertices1
450 md2.(model_fields{i})=field(pos_node,:);
451 elseif (fieldsize(1)==numberofvertices1+1)
452 md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
[13857]453 %size = number of elements * n
[13692]454 elseif fieldsize(1)==numberofelements1
455 md2.(model_fields{i})=field(pos_elem,:);
[21428]456 elseif (fieldsize(1)==numberofelements1+1)
457 md2.(model_fields{i})=[field(pos_elem,:); field(end,:)];
[13692]458 end
459 end
460 end
[13005]461
[13692]462 %modify some specific fields
[13005]463
[13692]464 %Mesh
465 md2.mesh.numberofelements=numberofelements2;
466 md2.mesh.numberofvertices=numberofvertices2;
467 md2.mesh.elements=elements_2;
[13005]468
[13692]469 %mesh.uppervertex mesh.lowervertex
[17558]470 if isa(md1.mesh,'mesh3dprisms'),
[13692]471 md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
472 pos=find(~isnan(md2.mesh.uppervertex));
473 md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));
[13005]474
[13692]475 md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
476 pos=find(~isnan(md2.mesh.lowervertex));
477 md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));
[13005]478
[13692]479 md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
480 pos=find(~isnan(md2.mesh.upperelements));
481 md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));
[13005]482
[13692]483 md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
484 pos=find(~isnan(md2.mesh.lowerelements));
485 md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
486 end
[13005]487
[13692]488 %Initial 2d mesh
[17558]489 if isa(md1.mesh,'mesh3dprisms'),
[13692]490 flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
491 pos_elem_2d=find(flag_elem_2d);
492 flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
493 pos_node_2d=find(flag_node_2d);
[13005]494
[13692]495 md2.mesh.numberofelements2d=length(pos_elem_2d);
496 md2.mesh.numberofvertices2d=length(pos_node_2d);
497 md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
498 md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
499 md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
500 md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));
[13005]501
[13692]502 md2.mesh.x2d=md1.mesh.x(pos_node_2d);
503 md2.mesh.y2d=md1.mesh.y(pos_node_2d);
504 end
[13005]505
[13692]506 %Edges
[17686]507 if(dimension(md.mesh)==2),
[17563]508 if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
509 %renumber first two columns
510 pos=find(md2.mesh.edges(:,4)~=-1);
511 md2.mesh.edges(: ,1)=Pnode(md2.mesh.edges(:,1));
512 md2.mesh.edges(: ,2)=Pnode(md2.mesh.edges(:,2));
513 md2.mesh.edges(: ,3)=Pelem(md2.mesh.edges(:,3));
514 md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
515 %remove edges when the 2 vertices are not in the domain.
516 md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
517 %Replace all zeros by -1 in the last two columns
518 pos=find(md2.mesh.edges(:,3)==0);
519 md2.mesh.edges(pos,3)=-1;
520 pos=find(md2.mesh.edges(:,4)==0);
521 md2.mesh.edges(pos,4)=-1;
522 %Invert -1 on the third column with last column (Also invert first two columns!!)
523 pos=find(md2.mesh.edges(:,3)==-1);
524 md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
525 md2.mesh.edges(pos,4)=-1;
526 values=md2.mesh.edges(pos,2);
527 md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
528 md2.mesh.edges(pos,1)=values;
529 %Finally remove edges that do not belong to any element
530 pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
531 md2.mesh.edges(pos,:)=[];
532 end
[13692]533 end
[13005]534
[13692]535 %Penalties
[15771]536 if ~isnan(md2.stressbalance.vertex_pairing),
537 for i=1:size(md1.stressbalance.vertex_pairing,1);
538 md2.stressbalance.vertex_pairing(i,:)=Pnode(md1.stressbalance.vertex_pairing(i,:));
[13692]539 end
[15771]540 md2.stressbalance.vertex_pairing=md2.stressbalance.vertex_pairing(find(md2.stressbalance.vertex_pairing(:,1)),:);
[13692]541 end
[15767]542 if ~isnan(md2.masstransport.vertex_pairing),
543 for i=1:size(md1.masstransport.vertex_pairing,1);
544 md2.masstransport.vertex_pairing(i,:)=Pnode(md1.masstransport.vertex_pairing(i,:));
[13692]545 end
[15767]546 md2.masstransport.vertex_pairing=md2.masstransport.vertex_pairing(find(md2.masstransport.vertex_pairing(:,1)),:);
[13692]547 end
[13005]548
[13692]549 %recreate segments
[20322]550 if isa(md1.mesh,'mesh2d') | isa(md1.mesh','mesh3dsurface'),
[13692]551 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
552 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
[19957]553 md2.mesh.segments=contourenvelope(md2.mesh);
[13692]554 md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
555 else
556 %First do the connectivity for the contourenvelope in 2d
557 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
558 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
[19957]559 segments=contourenvelope(md2.mesh);
[17565]560 md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(segments(:,1:2))=1;
[13692]561 md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
562 %Then do it for 3d as usual
563 md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
564 md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
565 end
[13005]566
[13692]567 %Boundary conditions: Dirichlets on new boundary
568 %Catch the elements that have not been extracted
569 orphans_elem=find(~flag_elem);
570 orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
571 %Figure out which node are on the boundary between md2 and md1
572 nodestoflag1=intersect(orphans_node,pos_node);
573 nodestoflag2=Pnode(nodestoflag1);
[15771]574 if numel(md1.stressbalance.spcvx)>1 & numel(md1.stressbalance.spcvy)>2 & numel(md1.stressbalance.spcvz)>2,
[13692]575 if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
[15771]576 md2.stressbalance.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2);
577 md2.stressbalance.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
[13692]578 else
[15771]579 md2.stressbalance.spcvx(nodestoflag2)=NaN;
580 md2.stressbalance.spcvy(nodestoflag2)=NaN;
[13692]581 disp(' ')
582 disp('!! extract warning: spc values should be checked !!')
583 disp(' ')
584 end
585 %put 0 for vz
[15771]586 md2.stressbalance.spcvz(nodestoflag2)=0;
[13692]587 end
588 if ~isnan(md1.thermal.spctemperature),
589 md2.thermal.spctemperature(nodestoflag2,1)=1;
590 end
[13005]591
[13692]592 %Results fields
593 if isstruct(md1.results),
594 md2.results=struct();
595 solutionfields=fields(md1.results);
596 for i=1:length(solutionfields),
[14230]597 if isstruct(md1.results.(solutionfields{i}))
598 %get subfields
599 solutionsubfields=fields(md1.results.(solutionfields{i}));
600 for j=1:length(solutionsubfields),
601 field=md1.results.(solutionfields{i}).(solutionsubfields{j});
602 if length(field)==numberofvertices1,
603 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
604 elseif length(field)==numberofelements1,
605 md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
606 else
607 md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
608 end
609 end
610 else
611 field=md1.results.(solutionfields{i});
[13692]612 if length(field)==numberofvertices1,
[14230]613 md2.results.(solutionfields{i})=field(pos_node);
[13692]614 elseif length(field)==numberofelements1,
[14230]615 md2.results.(solutionfields{i})=field(pos_elem);
[13692]616 else
[14230]617 md2.results.(solutionfields{i})=field;
[13692]618 end
619 end
620 end
621 end
[13005]622
[21808]623 %OutputDefinitions fields
624 for i=1:length(md1.outputdefinition.definitions),
625 if isobject(md1.outputdefinition.definitions{i})
626 %get subfields
627 solutionsubfields=fields(md1.outputdefinition.definitions{i});
628 for j=1:length(solutionsubfields),
629 field=md1.outputdefinition.definitions{i}.(solutionsubfields{j});
630 if length(field)==numberofvertices1,
631 md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_node);
632 elseif length(field)==numberofelements1,
633 md2.outputdefinition.definitions{i}.(solutionsubfields{j})=field(pos_elem);
634 end
635 end
636 end
637 end
638
[13692]639 %Keep track of pos_node and pos_elem
640 md2.mesh.extractedvertices=pos_node;
641 md2.mesh.extractedelements=pos_elem;
642 end % }}}
643 function md = extrude(md,varargin) % {{{
644 %EXTRUDE - vertically extrude a 2d mesh
645 %
646 % vertically extrude a 2d mesh and create corresponding 3d mesh.
647 % The vertical distribution can:
648 % - follow a polynomial law
649 % - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
650 % - be discribed by a list of coefficients (between 0 and 1)
651 %
652 %
653 % Usage:
654 % md=extrude(md,numlayers,extrusionexponent);
655 % md=extrude(md,numlayers,lowerexponent,upperexponent);
656 % md=extrude(md,listofcoefficients);
657 %
658 % Example:
[18216]659 % md=extrude(md,15,1.3);
660 % md=extrude(md,15,1.3,1.2);
[13692]661 % md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
662 %
663 % See also: MODELEXTRACT, COLLAPSE
[13005]664
[13692]665 %some checks on list of arguments
666 if ((nargin>4) | (nargin<2) | (nargout~=1)),
667 help extrude;
668 error('extrude error message');
669 end
[13005]670
[13692]671 %Extrude the mesh
672 if nargin==2, %list of coefficients
673 clist=varargin{1};
674 if any(clist<0) | any(clist>1),
675 error('extrusioncoefficients must be between 0 and 1');
676 end
677 extrusionlist=sort(unique([clist(:);0;1]));
678 numlayers=length(extrusionlist);
679 elseif nargin==3, %one polynomial law
680 if varargin{2}<=0,
681 help extrude;
682 error('extrusionexponent must be >=0');
683 end
684 numlayers=varargin{1};
685 extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
686 elseif nargin==4, %two polynomial laws
687 numlayers=varargin{1};
688 lowerexp=varargin{2};
689 upperexp=varargin{3};
[13005]690
[13692]691 if varargin{2}<=0 | varargin{3}<=0,
692 help extrude;
693 error('lower and upper extrusionexponents must be >=0');
694 end
[13005]695
[13692]696 lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
697 upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
698 extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));
[13005]699
[13692]700 end
[13005]701
[13692]702 if numlayers<2,
703 error('number of layers should be at least 2');
704 end
[17686]705 if strcmp(md.mesh.domaintype(),'3D')
[13692]706 error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
707 end
[13005]708
[13692]709 %Initialize with the 2d mesh
[17558]710 mesh2d = md.mesh;
711 md.mesh=mesh3dprisms();
712 md.mesh.x = mesh2d.x;
713 md.mesh.y = mesh2d.y;
714 md.mesh.elements = mesh2d.elements;
715 md.mesh.numberofelements = mesh2d.numberofelements;
716 md.mesh.numberofvertices = mesh2d.numberofvertices;
717
718 md.mesh.lat = mesh2d.lat;
719 md.mesh.long = mesh2d.long;
[18558]720 md.mesh.epsg = mesh2d.epsg;
[17558]721
722 md.mesh.vertexonboundary = mesh2d.vertexonboundary;
723 md.mesh.vertexconnectivity = mesh2d.vertexconnectivity;
724 md.mesh.elementconnectivity = mesh2d.elementconnectivity;
725 md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;
726
727 md.mesh.extractedvertices = mesh2d.extractedvertices;
728 md.mesh.extractedelements = mesh2d.extractedelements;
729
[13692]730 x3d=[];
731 y3d=[];
732 z3d=[]; %the lower node is on the bed
733 thickness3d=md.geometry.thickness; %thickness and bed for these nodes
[17590]734 bed3d=md.geometry.base;
[13005]735
[13692]736 %Create the new layers
737 for i=1:numlayers,
738 x3d=[x3d; md.mesh.x];
739 y3d=[y3d; md.mesh.y];
740 %nodes are distributed between bed and surface accordingly to the given exponent
741 z3d=[z3d; bed3d+thickness3d*extrusionlist(i)];
742 end
743 number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]744
[13692]745 %Extrude elements
746 elements3d=[];
747 for i=1:numlayers-1,
748 elements3d=[elements3d;[md.mesh.elements+(i-1)*md.mesh.numberofvertices md.mesh.elements+i*md.mesh.numberofvertices]]; %Create the elements of the 3d mesh for the non extruded part
749 end
750 number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh
[13005]751
[13692]752 %Keep a trace of lower and upper nodes
[17590]753 lowervertex=NaN*ones(number_nodes3d,1);
754 uppervertex=NaN*ones(number_nodes3d,1);
755 lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
756 uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
757 md.mesh.lowervertex=lowervertex;
758 md.mesh.uppervertex=uppervertex;
[13005]759
[13692]760 %same for lower and upper elements
[17590]761 lowerelements=NaN*ones(number_el3d,1);
762 upperelements=NaN*ones(number_el3d,1);
763 lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
764 upperelements(1:(numlayers-2)*md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)*md.mesh.numberofelements;
765 md.mesh.lowerelements=lowerelements;
766 md.mesh.upperelements=upperelements;
[13005]767
[13692]768 %Save old mesh
769 md.mesh.x2d=md.mesh.x;
770 md.mesh.y2d=md.mesh.y;
771 md.mesh.elements2d=md.mesh.elements;
772 md.mesh.numberofelements2d=md.mesh.numberofelements;
773 md.mesh.numberofvertices2d=md.mesh.numberofvertices;
[13005]774
[13692]775 %Build global 3d mesh
776 md.mesh.elements=elements3d;
777 md.mesh.x=x3d;
778 md.mesh.y=y3d;
779 md.mesh.z=z3d;
780 md.mesh.numberofelements=number_el3d;
781 md.mesh.numberofvertices=number_nodes3d;
782 md.mesh.numberoflayers=numlayers;
[13005]783
[13692]784 %Ok, now deal with the other fields from the 2d mesh:
[13005]785
[19048]786 %bedinfo and surface info
787 md.mesh.vertexonbase=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
788 md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
789 md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
790
[13692]791 %lat long
792 md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
793 md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');
[13005]794
[19048]795 md.geometry=extrude(md.geometry,md);
796 md.friction = extrude(md.friction,md);
797 md.inversion = extrude(md.inversion,md);
[19527]798 md.smb = extrude(md.smb,md);
[19048]799 md.initialization = extrude(md.initialization,md);
[13005]800
[19050]801 md.flowequation=md.flowequation.extrude(md);
[19048]802 md.stressbalance=extrude(md.stressbalance,md);
[19050]803 md.thermal=md.thermal.extrude(md);
804 md.masstransport=md.masstransport.extrude(md);
[20460]805 md.levelset=extrude(md.levelset,md);
[19048]806 md.calving=extrude(md.calving,md);
807 md.hydrology = extrude(md.hydrology,md);
[13005]808
[13692]809 %connectivity
[17991]810 if ~isnan(md.mesh.elementconnectivity)
811 md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
812 md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
813 for i=2:numlayers-1,
814 md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)...
815 =md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
816 end
817 md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;
[13692]818 end
[13005]819
[19048]820 md.materials=extrude(md.materials,md);
821 md.damage=extrude(md.damage,md);
822 md.mask=extrude(md.mask,md);
823 md.qmu=extrude(md.qmu,md);
824 md.basalforcings=extrude(md.basalforcings,md);
[21808]825 md.outputdefinition=extrude(md.outputdefinition,md);
[13005]826
[13692]827 %increase connectivity if less than 25:
828 if md.mesh.average_vertex_connectivity<=25,
829 md.mesh.average_vertex_connectivity=100;
830 end
[13005]831 end % }}}
[13692]832 function md = structtomodel(md,structmd) % {{{
[8952]833
[13692]834 if ~isstruct(structmd) error('input model is not a structure'); end
[8952]835
[13692]836 %loaded model is a struct, initialize output and recover all fields
837 md = structtoobj(model,structmd);
[8952]838
[13692]839 %Old field now classes
840 if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
841 if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end
[10452]842
[13692]843 %Field name change
844 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
845 if isfield(structmd,'p'), md.friction.p=structmd.p; end
846 if isfield(structmd,'q'), md.friction.q=structmd.p; end
[18378]847 if isfield(structmd,'melting'), md.basalforcings.floatingice_melting_rate=structmd.melting; end
[18068]848 if isfield(structmd,'melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.melting_rate; end
[18378]849 if isfield(structmd,'melting_rate'), md.basalforcings.groundedice_melting_rate=structmd.melting_rate; end
[19527]850 if isfield(structmd,'accumulation'), md.smb.mass_balance=structmd.accumulation; end
[13692]851 if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
852 if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
853 if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
854 if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
[17610]855 if isfield(structmd,'gridonbase'), md.mesh.vertexonbase=structmd.gridonbase; end
[13692]856 if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
857 if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
858 if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
[14621]859 if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.toolkits=structmd.petscoptions; end
[13692]860 if isfield(structmd,'g'), md.constants.g=structmd.g; end
861 if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
[19527]862 if isfield(structmd,'surface_mass_balance'), md.smb.mass_balance=structmd.surface_mass_balance; end
[18068]863 if isfield(structmd,'basal_melting_rate'), md.basalforcings.floatingice_melting_rate=structmd.basal_melting_rate; end
[13692]864 if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
865 if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
866 if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
867 if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
868 if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
869 if isfield(structmd,'riftproperties'), %old implementation
870 md.rifts=rifts();
871 md.rifts.riftproperties=structmd.riftproperties;
872 md.rifts.riftstruct=structmd.rifts;
873 md.rifts.riftproperties=structmd.riftinfo;
874 end
875 if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
876 if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
877 if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
878 if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
879 if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
880 if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
881 if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
882 if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
883 if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
884 if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
885 if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
886 if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
887 if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
888 if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
889 if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
890 if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
891 if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
892 if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
893 if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
894 if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
895 if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
896 if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
[15767]897 if isfield(structmd,'spcthickness'), md.masstransport.spcthickness=structmd.spcthickness; end
898 if isfield(structmd,'artificial_diffusivity'), md.masstransport.stabilization=structmd.artificial_diffusivity; end
899 if isfield(structmd,'hydrostatic_adjustment'), md.masstransport.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
900 if isfield(structmd,'penalties'), md.masstransport.vertex_pairing=structmd.penalties; end
901 if isfield(structmd,'penalty_offset'), md.masstransport.penalty_factor=structmd.penalty_offset; end
[13692]902 if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
903 if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
904 if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
905 if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
[16160]906 if isfield(structmd,'rheology_Z'), md.damage.D=(1-structmd.rheology_Z); end
[13692]907 if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
908 if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
909 if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
[15564]910 if isfield(structmd,'isSIA'), md.flowequation.isSIA=structmd.isSIA; end
911 if isfield(structmd,'isFS'), md.flowequation.isFS=structmd.isFS; end
[13692]912 if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
913 if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
914 if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
915 if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
[15771]916 if isfield(structmd,'isdiagnostic'), md.transient.isstressbalance=structmd.isdiagnostic; end
[15768]917 if isfield(structmd,'isprognostic'), md.transient.ismasstransport=structmd.isprognostic; end
[13692]918 if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
919 if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
920 if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
921 if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
922 if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
923 if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
924 if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
925 if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
926 if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
927 if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
928 if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
929 if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
930 if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
931 if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
932 if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
933 if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
934 if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
935 if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
936 if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
937 if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
[17590]938 if isfield(structmd,'bed'), md.geometry.base=structmd.bed; end
[13692]939 if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
[17590]940 if isfield(structmd,'bathymetry'), md.geometry.bed=structmd.bathymetry; end
[13692]941 if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
942 if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
943 if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
944 if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
945 if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
946 if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
947 if isfield(structmd,'long'), md.mesh.long=structmd.long; end
948 if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
949 if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
950 if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
951 if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
952 if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
953 if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
954 if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
955 if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
956 if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
957 if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
958 if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
959 if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
960 if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
961 if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
962 if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
963 if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
[17610]964 if isfield(structmd,'nodeonbase'), md.mesh.vertexonbase=structmd.nodeonbase; end
[13692]965 if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
966 if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
967 if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
968 if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
[13717]969 if isfield(structmd,'edges'),
970 md.mesh.edges=structmd.edges;
971 md.mesh.edges(isnan(md.mesh.edges))=-1;
972 end
[13692]973 if isfield(structmd,'y'), md.mesh.y=structmd.y; end
974 if isfield(structmd,'x'), md.mesh.x=structmd.x; end
975 if isfield(structmd,'z'), md.mesh.z=structmd.z; end
[15771]976 if isfield(structmd,'diagnostic_ref'), md.stressbalance.referential=structmd.diagnostic_ref; end
[13692]977 if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
978 if isfield(structmd,'part'); md.qmu.partition=structmd.part; end
[13646]979
[13692]980 if isnumeric(md.verbose),
981 md.verbose=verbose;
982 end
[15768]983
[13692]984 if isfield(structmd,'spcvelocity'),
[15771]985 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
986 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
987 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
988 pos=find(structmd.spcvelocity(:,1)); md.stressbalance.spcvx(pos)=structmd.spcvelocity(pos,4);
989 pos=find(structmd.spcvelocity(:,2)); md.stressbalance.spcvy(pos)=structmd.spcvelocity(pos,5);
990 pos=find(structmd.spcvelocity(:,3)); md.stressbalance.spcvz(pos)=structmd.spcvelocity(pos,6);
[13692]991 end
992 if isfield(structmd,'spcvx'),
[15771]993 md.stressbalance.spcvx=NaN*ones(md.mesh.numberofvertices,1);
994 pos=find(~isnan(structmd.spcvx)); md.stressbalance.spcvx(pos)=structmd.spcvx(pos);
[13692]995 end
996 if isfield(structmd,'spcvy'),
[15771]997 md.stressbalance.spcvy=NaN*ones(md.mesh.numberofvertices,1);
998 pos=find(~isnan(structmd.spcvy)); md.stressbalance.spcvy(pos)=structmd.spcvy(pos);
[13692]999 end
1000 if isfield(structmd,'spcvz'),
[15771]1001 md.stressbalance.spcvz=NaN*ones(md.mesh.numberofvertices,1);
1002 pos=find(~isnan(structmd.spcvz)); md.stressbalance.spcvz(pos)=structmd.spcvz(pos);
[13692]1003 end
[14620]1004 if isfield(structmd,'pressureload'),
1005 if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
[15771]1006 pos=find(structmd.pressureload(:,end)==120); md.stressbalance.icefront(pos,end)=0;
1007 pos=find(structmd.pressureload(:,end)==118); md.stressbalance.icefront(pos,end)=1;
1008 pos=find(structmd.pressureload(:,end)==119); md.stressbalance.icefront(pos,end)=2;
[14620]1009 end
[13692]1010 end
1011 if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
1012 pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
1013 pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
1014 pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
1015 pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
1016 pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
1017 pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
1018 pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
1019 pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
1020 end
1021 if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
1022 pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
1023 pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
1024 pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
1025 pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
1026 pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
1027 pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
1028 pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
1029 pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
1030 end
1031 if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
1032 if (structmd.rheology_law==272), md.materials.rheology_law='None'; end
1033 if (structmd.rheology_law==368), md.materials.rheology_law='Paterson'; end
1034 if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
1035 end
1036 if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
1037 if (structmd.groundingline_migration==272), md.groundingline.migration='None'; end
[17941]1038 if (structmd.groundingline_migration==273), md.groundingline.migration='AggressiveMigration'; end
[13692]1039 if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
1040 end
1041 if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
1042 if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
1043 if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
1044 if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
1045 end
1046 if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
1047 pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
1048 pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
1049 pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
1050 pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
1051 pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
1052 pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
1053 pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
1054 pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
1055 pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
1056 end
[11659]1057
[13692]1058 if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
1059 md.thermal.stabilization=2;
[15767]1060 md.masstransport.stabilization=1;
[13692]1061 md.balancethickness.stabilization=1;
1062 end
[15767]1063 if isnumeric(md.masstransport.hydrostatic_adjustment)
1064 if md.masstransport.hydrostatic_adjustment==269,
1065 md.masstransport.hydrostatic_adjustment='Incremental';
[13692]1066 else
[15767]1067 md.masstransport.hydrostatic_adjustment='Absolute';
[13692]1068 end
1069 end
[8952]1070
[13692]1071 %New fields
[19124]1072 if ~isfield(structmd,'upperelements') & isa(md.mesh,'mesh3dprisms')
[13692]1073 md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
1074 md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
1075 end
[19124]1076 if ~isfield(structmd,'lowerelements') & isa(md.mesh,'mesh3dprisms')
[13692]1077 md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
1078 md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
1079 end
1080 if ~isfield(structmd,'diagnostic_ref');
[15771]1081 md.stressbalance.referential=NaN*ones(md.mesh.numberofvertices,6);
[13692]1082 end
[14529]1083 if ~isfield(structmd,'loadingforce');
[15771]1084 md.stressbalance.loadingforce=0*ones(md.mesh.numberofvertices,3);
[14529]1085 end
[15768]1086
1087 %2013 August 9
1088 if isfield(structmd,'prognostic') & isa(structmd.prognostic,'prognostic'),
1089 disp('Recovering old prognostic class');
1090 md.masstransport=masstransport(structmd.prognostic);
1091 end
[15771]1092 %2013 August 9
[15775]1093 if isfield(structmd,'diagnostic') & (isa(structmd.diagnostic,'diagnostic') || isa(structmd.diagnostic,'stressbalance')),
[15771]1094 disp('Recovering old diagnostic class');
[15775]1095 md.stressbalance=stressbalance(structmd.diagnostic);
[15771]1096 end
[19642]1097 %2014 January 9th
[21148]1098 if isfield(structmd,'surfaceforcings') & isa(md.smb,'surfaceforcings'),
[19642]1099 disp('Recovering old surfaceforcings class');
1100 mass_balance=structmd.surfaceforcings.mass_balance;
1101 md.smb=SMB();
1102 md.smb.mass_balance=mass_balance;
1103 end
1104 %2015 September 10
[21148]1105 if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMB'),
[19642]1106 disp('Recovering old SMB class');
1107 md.smb=SMBforcing(structmd.surfaceforcings);
1108 end
[21148]1109 if isfield(structmd,'surfaceforcings') & isa(structmd.surfaceforcings,'SMBhenning'),
1110 disp('Recovering old SMBhenning class');
1111 md.smb=SMBhenning(structmd.surfaceforcings);
1112 end
[19642]1113
[13692]1114 end% }}}
1115 function md = setdefaultparameters(md) % {{{
[8926]1116
[13692]1117 %initialize subclasses
[17558]1118 md.mesh = mesh2d();
[13692]1119 md.mask = mask();
1120 md.constants = constants();
1121 md.geometry = geometry();
1122 md.initialization = initialization();
[19527]1123 md.smb = SMBforcing();
[13692]1124 md.basalforcings = basalforcings();
1125 md.friction = friction();
1126 md.rifts = rifts();
[19984]1127 md.slr = slr();
[13692]1128 md.timestepping = timestepping();
1129 md.groundingline = groundingline();
1130 md.materials = matice();
[16160]1131 md.damage = damage();
[13692]1132 md.flowequation = flowequation();
1133 md.debug = debug();
[14558]1134 md.verbose = verbose();
[13692]1135 md.settings = settings();
[17932]1136 md.toolkits = toolkits();
[13692]1137 md.cluster = generic();
1138 md.balancethickness = balancethickness();
[17079]1139 md.stressbalance = stressbalance();
[14555]1140 md.hydrology = hydrologyshreve();
[17079]1141 md.masstransport = masstransport();
[13692]1142 md.thermal = thermal();
1143 md.steadystate = steadystate();
1144 md.transient = transient();
[20460]1145 md.levelset = levelset();
[18757]1146 md.calving = calving();
[21584]1147 md.gia = giaivins();
[21260]1148 md.esa = esa();
[13692]1149 md.autodiff = autodiff();
1150 md.inversion = inversion();
1151 md.qmu = qmu();
[21674]1152 md.amr = amr();
[13692]1153 md.radaroverlay = radaroverlay();
1154 md.results = struct();
[16388]1155 md.outputdefinition = outputdefinition();
[13692]1156 md.miscellaneous = miscellaneous();
1157 md.private = private();
1158 end
1159 %}}}
[17483]1160 function md = tetras(md,varargin) % {{{
1161 %TETRAS - split 3d prismatic mesh into 3 tetrahedrons
1162 %
1163 % Usage:
1164 % md=tetra(md)
1165
1166 if ~isa(md.mesh,'mesh3dprisms')
1167 error('mesh is not a 3d prismatic mesh');
1168 end
1169
1170 %Initialize tetra mesh
1171 md.mesh=mesh3dtetras(md.mesh);
1172
[17754]1173 %Subdivision from Philipp Furnstahl (http://studierstube.icg.tugraz.at/thesis/fuernstahl_thesis.pdf)
1174 steiner = 0;
1175 nbv = md.mesh.numberofvertices;
1176 nbt = 3*md.mesh.numberofelements;
1177 elements = zeros(nbt,4);
1178 for i=1:md.mesh.numberofelements
1179 v1=md.mesh.elements(i,1); v2=md.mesh.elements(i,2); v3=md.mesh.elements(i,3);
1180 v4=md.mesh.elements(i,4); v5=md.mesh.elements(i,5); v6=md.mesh.elements(i,6);
1181 if(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1182 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1183 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1184 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1185 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1186 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1187 elements(3*(i-1)+2,:) = [v1 v2 v4 v7];
1188 elements(3*(i-1)+3,:) = [v2 v4 v5 v7];
1189 elements(end+1,:) = [v2 v3 v5 v7];
1190 elements(end+1,:) = [v3 v5 v6 v7];
1191 elements(end+1,:) = [v1 v3 v6 v7];
1192 elements(end+1,:) = [v1 v4 v6 v7];
1193 elements(end+1,:) = [v4 v5 v6 v7];
1194 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1195 elements(3*(i-1)+1,:) = [v1 v2 v4 v6];
1196 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1197 elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1198 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1199 elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1200 elements(3*(i-1)+2,:) = [v2 v3 v4 v5];
1201 elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1202 elseif(min(v2,v4)<min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1203 elements(3*(i-1)+1,:) = [v1 v2 v3 v4];
1204 elements(3*(i-1)+2,:) = [v2 v4 v5 v6];
1205 elements(3*(i-1)+3,:) = [v2 v3 v4 v6];
[18142]1206 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
[17754]1207 elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1208 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1209 elements(3*(i-1)+3,:) = [v1 v3 v5 v6];
1210 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)>min(v2,v6)),
1211 elements(3*(i-1)+1,:) = [v1 v4 v5 v6];
1212 elements(3*(i-1)+2,:) = [v1 v2 v5 v6];
1213 elements(3*(i-1)+3,:) = [v1 v2 v3 v6];
1214 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)<min(v2,v6)),
1215 elements(3*(i-1)+1,:) = [v1 v3 v4 v5];
1216 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1217 elements(3*(i-1)+3,:) = [v3 v4 v5 v6];
1218 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)<min(v3,v4) & min(v3,v5)<min(v2,v6)),
1219 elements(3*(i-1)+1,:) = [v1 v5 v6 v4];
1220 elements(3*(i-1)+2,:) = [v1 v2 v3 v5];
1221 elements(3*(i-1)+3,:) = [v5 v6 v3 v1];
1222 elseif(min(v2,v4)>min(v1,v5) & min(v1,v6)>min(v3,v4) & min(v3,v5)>min(v2,v6)),
1223 steiner = steiner+1; nbv = nbv+1; nbt = nbt+5; v7 = nbv;
1224 md.mesh.x=[md.mesh.x; mean(md.mesh.x(md.mesh.elements(i,:)))];
1225 md.mesh.y=[md.mesh.y; mean(md.mesh.y(md.mesh.elements(i,:)))];
1226 md.mesh.z=[md.mesh.z; mean(md.mesh.z(md.mesh.elements(i,:)))];
1227 elements(3*(i-1)+1,:) = [v1 v2 v3 v7];
1228 elements(3*(i-1)+2,:) = [v1 v4 v5 v7];
1229 elements(3*(i-1)+3,:) = [v1 v2 v5 v7];
1230 elements(end+1,:) = [v2 v5 v6 v7];
1231 elements(end+1,:) = [v2 v3 v6 v7];
1232 elements(end+1,:) = [v3 v4 v6 v7];
1233 elements(end+1,:) = [v1 v3 v4 v7];
1234 elements(end+1,:) = [v4 v5 v6 v7];
1235 else
1236 error('Case not supported'); %not supposed to happen!
1237 end
[17774]1238 %Reorder elements to make sure they are direct
1239 for j=1:3
1240 element = elements(3*(i-1)+j,:);
1241 matrix = [md.mesh.x(element), md.mesh.y(element), md.mesh.z(element), ones(4,1)];
1242 if det(matrix)>0,
1243 elements(3*(i-1)+j,1)=element(2);
1244 elements(3*(i-1)+j,2)=element(1);
1245 end
1246 end
[17754]1247 end
1248 %%Split in 3 tetras
1249 %subelement1 = [1 2 3 5];
1250 %subelement2 = [4 6 5 1];
1251 %subelement3 = [5 6 3 1];
1252 %elements=[md.mesh.elements(:,subelement1);md.mesh.elements(:,subelement2);md.mesh.elements(:,subelement3)];
[17774]1253 if steiner==0,
1254 disp('No Steiner point required to split prismatic mesh into tets');
1255 else
1256 disp([num2str(steiner) ' Steiner points had to be included'])
1257 error('Steiner point not supported yet');
1258 end
[17754]1259
[17483]1260 pos_elements = repmat([1:md.mesh.numberofelements]',3,1);
1261
1262 md.mesh.elements=elements;
1263 md.mesh.numberofelements=size(elements,1);
1264
1265 %p and q (same deal, except for element that are on the bedrock: )
[17774]1266 if ~isnan(md.friction.p),
1267 md.friction.p=md.friction.p(pos_elements);
1268 md.friction.q=md.friction.q(pos_elements);
1269 end
[17483]1270
1271 %elementstype
1272 if ~isnan(md.flowequation.element_equation)
1273 oldelements_type=md.flowequation.element_equation;
1274 md.flowequation.element_equation=md.flowequation.element_equation(pos_elements);
1275 end
1276
1277 %connectivity
1278 md.mesh.elementconnectivity=NaN;
1279
1280 %materials
[17774]1281 if ~isnan(md.materials.rheology_n),
1282 md.materials.rheology_n=md.materials.rheology_n(pos_elements);
1283 end
[17483]1284
1285 %increase connectivity if less than 25:
1286 if md.mesh.average_vertex_connectivity<=25,
1287 md.mesh.average_vertex_connectivity=100;
1288 end
1289 end % }}}
[19040]1290 function disp(self) % {{{
1291 disp(sprintf('%19s: %-22s -- %s','mesh' ,['[1x1 ' class(self.mesh) ']'],'mesh properties'));
1292 disp(sprintf('%19s: %-22s -- %s','mask' ,['[1x1 ' class(self.mask) ']'],'defines grounded and floating elements'));
1293 disp(sprintf('%19s: %-22s -- %s','geometry' ,['[1x1 ' class(self.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
1294 disp(sprintf('%19s: %-22s -- %s','constants' ,['[1x1 ' class(self.constants) ']'],'physical constants'));
[19527]1295 disp(sprintf('%19s: %-22s -- %s','smb' ,['[1x1 ' class(self.smb) ']'],'surface mass balance'));
[19040]1296 disp(sprintf('%19s: %-22s -- %s','basalforcings' ,['[1x1 ' class(self.basalforcings) ']'],'bed forcings'));
1297 disp(sprintf('%19s: %-22s -- %s','materials' ,['[1x1 ' class(self.materials) ']'],'material properties'));
1298 disp(sprintf('%19s: %-22s -- %s','damage' ,['[1x1 ' class(self.damage) ']'],'parameters for damage evolution solution'));
1299 disp(sprintf('%19s: %-22s -- %s','friction' ,['[1x1 ' class(self.friction) ']'],'basal friction/drag properties'));
1300 disp(sprintf('%19s: %-22s -- %s','flowequation' ,['[1x1 ' class(self.flowequation) ']'],'flow equations'));
1301 disp(sprintf('%19s: %-22s -- %s','timestepping' ,['[1x1 ' class(self.timestepping) ']'],'time stepping for transient models'));
1302 disp(sprintf('%19s: %-22s -- %s','initialization' ,['[1x1 ' class(self.initialization) ']'],'initial guess/state'));
1303 disp(sprintf('%19s: %-22s -- %s','rifts' ,['[1x1 ' class(self.rifts) ']'],'rifts properties'));
[19984]1304 disp(sprintf('%19s: %-22s -- %s','slr' ,['[1x1 ' class(self.slr) ']'],'slr forcings'));
[19040]1305 disp(sprintf('%19s: %-22s -- %s','debug' ,['[1x1 ' class(self.debug) ']'],'debugging tools (valgrind, gprof)'));
1306 disp(sprintf('%19s: %-22s -- %s','verbose' ,['[1x1 ' class(self.verbose) ']'],'verbosity level in solve'));
1307 disp(sprintf('%19s: %-22s -- %s','settings' ,['[1x1 ' class(self.settings) ']'],'settings properties'));
1308 disp(sprintf('%19s: %-22s -- %s','toolkits' ,['[1x1 ' class(self.toolkits) ']'],'PETSc options for each solution'));
1309 disp(sprintf('%19s: %-22s -- %s','cluster' ,['[1x1 ' class(self.cluster) ']'],'cluster parameters (number of cpus...)'));
1310 disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(self.balancethickness) ']'],'parameters for balancethickness solution'));
1311 disp(sprintf('%19s: %-22s -- %s','stressbalance' ,['[1x1 ' class(self.stressbalance) ']'],'parameters for stressbalance solution'));
1312 disp(sprintf('%19s: %-22s -- %s','groundingline' ,['[1x1 ' class(self.groundingline) ']'],'parameters for groundingline solution'));
1313 disp(sprintf('%19s: %-22s -- %s','hydrology' ,['[1x1 ' class(self.hydrology) ']'],'parameters for hydrology solution'));
1314 disp(sprintf('%19s: %-22s -- %s','masstransport' ,['[1x1 ' class(self.masstransport) ']'],'parameters for masstransport solution'));
1315 disp(sprintf('%19s: %-22s -- %s','thermal' ,['[1x1 ' class(self.thermal) ']'],'parameters for thermal solution'));
1316 disp(sprintf('%19s: %-22s -- %s','steadystate' ,['[1x1 ' class(self.steadystate) ']'],'parameters for steadystate solution'));
1317 disp(sprintf('%19s: %-22s -- %s','transient' ,['[1x1 ' class(self.transient) ']'],'parameters for transient solution'));
[21544]1318 disp(sprintf('%19s: %-22s -- %s','levelset' ,['[1x1 ' class(self.levelset) ']'],'parameters for moving boundaries (level-set method)'));
[19040]1319 disp(sprintf('%19s: %-22s -- %s','calving' ,['[1x1 ' class(self.calving) ']'],'parameters for calving'));
[21584]1320 disp(sprintf('%19s: %-22s -- %s','gia' ,['[1x1 ' class(self.gia) ']'],'parameters for gia solution'));
[21260]1321 disp(sprintf('%19s: %-22s -- %s','esa' ,['[1x1 ' class(self.esa) ']'],'parameters for elastic adjustment solution'));
[19040]1322 disp(sprintf('%19s: %-22s -- %s','autodiff' ,['[1x1 ' class(self.autodiff) ']'],'automatic differentiation parameters'));
1323 disp(sprintf('%19s: %-22s -- %s','inversion' ,['[1x1 ' class(self.inversion) ']'],'parameters for inverse methods'));
1324 disp(sprintf('%19s: %-22s -- %s','qmu' ,['[1x1 ' class(self.qmu) ']'],'dakota properties'));
[21674]1325 disp(sprintf('%19s: %-22s -- %s','amr' ,['[1x1 ' class(self.amr) ']'],'adaptive mesh refinement properties'));
[19040]1326 disp(sprintf('%19s: %-22s -- %s','outputdefinition',['[1x1 ' class(self.outputdefinition) ']'],'output definition'));
1327 disp(sprintf('%19s: %-22s -- %s','results' ,['[1x1 ' class(self.results) ']'],'model results'));
1328 disp(sprintf('%19s: %-22s -- %s','radaroverlay' ,['[1x1 ' class(self.radaroverlay) ']'],'radar image for plot overlay'));
1329 disp(sprintf('%19s: %-22s -- %s','miscellaneous' ,['[1x1 ' class(self.miscellaneous) ']'],'miscellaneous fields'));
[13692]1330 end % }}}
[19040]1331 function memory(self) % {{{
[15106]1332
[14611]1333 disp(sprintf('\nMemory imprint:\n'));
[14307]1334
[14603]1335 fields=properties('model');
1336 mem=0;
[15106]1337
[14603]1338 for i=1:length(fields),
[19040]1339 field=self.(fields{i});
[14603]1340 s=whos('field');
1341 mem=mem+s.bytes/1e6;
[14611]1342 disp(sprintf('%19s: %6.2f Mb',fields{i},s.bytes/1e6));
[14307]1343 end
[14603]1344 disp(sprintf('%19s--%10s','--------------','--------------'));
1345 disp(sprintf('%19s: %g Mb','Total',mem));
[14307]1346 end % }}}
[19040]1347 function netcdf(self,filename) % {{{
[14603]1348 %NETCDF - save model as netcdf
1349 %
1350 % Usage:
1351 % netcdf(md,filename)
1352 %
1353 % Example:
1354 % netcdf(md,'model.nc');
1355
1356 disp('Saving model as NetCDF');
1357 %1. Create NetCDF file
1358 ncid=netcdf.create(filename,'CLOBBER');
1359 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Conventions','CF-1.4');
[19040]1360 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['ISSM model (' self.miscellaneous.name ')']);
[14603]1361 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Author',getenv('USER'));
1362 netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',datestr(now));
1363
[14611]1364 %Preallocate variable id, needed to write variables in netcdf file
[14631]1365 var_id=zeros(1000,1);%preallocate
[14609]1366
1367 for step=1:2,
1368 counter=0;
[19040]1369 [var_id,counter]=structtonc(ncid,'md',self,0,var_id,counter,step);
[14609]1370 if step==1, netcdf.endDef(ncid); end
[14603]1371 end
[14611]1372
[14631]1373 if counter>1000,
1374 warning(['preallocation of var_id need to be updated from ' num2str(1000) ' to ' num2str(counter)]);
[14609]1375 end
1376
1377 netcdf.close(ncid)
[14603]1378 end % }}}
[19040]1379 function xylim(self) % {{{
[14405]1380
[19040]1381 xlim([min(self.mesh.x) max(self.mesh.x)]);
1382 ylim([min(self.mesh.y) max(self.mesh.y)])
[14405]1383 end % }}}
[15316]1384 function md=upload(md) % {{{
1385 %the goal of this routine is to upload the model onto a server, and to empty it.
1386 %So first, save the model with a unique name and upload the file to the server:
1387 random_part=fix(rand(1)*10000);
1388 id=[md.miscellaneous.name '-' regexprep(datestr(now),'[^\w'']','') '-' num2str(random_part) '-' getenv('USER') '-' oshostname() '.upload'];
1389 eval(['save ' id ' md']);
1390
1391 %Now, upload the file:
1392 issmscpout(md.settings.upload_server,md.settings.upload_path,md.settings.upload_login,md.settings.upload_port,{id},1);
1393
1394 %Now, empty this model of everything except settings, and record name of file we just uploaded!
1395 settings_back=md.settings;
1396 md=model();
1397 md.settings=settings_back;
1398 md.settings.upload_filename=id;
1399
1400 %get locally rid of file that was uploaded
1401 eval(['delete ' id]);
1402
1403 end % }}}
1404 function md=download(md) % {{{
[15643]1405
[15316]1406 %the goal of this routine is to download the internals of the current model from a server, because
1407 %this model is empty, except for the settings which tell us where to go and find this model!
[15643]1408
[15316]1409 %Download the file:
1410 issmscpin(md.settings.upload_server, md.settings.upload_login, md.settings.upload_port, md.settings.upload_path, {md.settings.upload_filename});
1411
1412 name=md.settings.upload_filename;
1413
1414 %Now, load this model:
1415 md=loadmodel(md.settings.upload_filename);
1416
1417 %get locally rid of file that was downloaded
1418 eval(['delete ' name]);
1419
1420 end % }}}
[19894]1421 function savemodeljs(md,modelname,websiteroot) % {{{
[19879]1422
1423 %the goal of this routine is to save the model as a javascript array that can be included in any html
1424 %file:
1425
1426 %disp:
[19894]1427 disp(['saving model ''' modelname ''' in file ' websiteroot '/js/' modelname '.js']);
[19879]1428
1429 %open file for writing and declare the model:
[19894]1430 fid=fopen([websiteroot '/js/' modelname '.js'],'w');
[19879]1431 fprintf(fid,'var %s=new model();\n',modelname);
1432
1433 %now go through all the classes and fwrite all the corresponding fields:
1434
1435 fields=properties('model');
1436 for i=1:length(fields),
1437 field=fields{i};
1438
1439 %Some properties do not need to be saved
[19894]1440 if ismember(field,{'results','cluster' }),
[19879]1441 continue;
1442 end
1443
1444 %Check that current field is an object
1445 if ~isobject(md.(field))
1446 error(['field ''' char(field) ''' is not an object']);
1447 end
1448
1449 %savemodeljs for current object
1450 %disp(['javascript saving ' field '...']);
1451 savemodeljs(md.(field),fid,modelname);
1452 end
1453
1454 %done, close file:
1455 fclose(fid);
1456 end
[13692]1457 end
[8926]1458 end
Note: See TracBrowser for help on using the repository browser.